4th International ICST Conference on Simulation Tools and Techniques

Research Article

Stability Analysis of Biological Network Topologies during Stochastic Simulation

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  • @INPROCEEDINGS{10.4108/icst.simutools.2011.245590,
        author={Davide Prandi and Tommaso Mazza},
        title={Stability Analysis of Biological Network Topologies during Stochastic Simulation},
        proceedings={4th International ICST Conference on Simulation Tools and Techniques},
        publisher={ICST},
        proceedings_a={SIMUTOOLS},
        year={2012},
        month={4},
        keywords={Graph algorithms Monte Carlo Biology and genetics},
        doi={10.4108/icst.simutools.2011.245590}
    }
    
  • Davide Prandi
    Tommaso Mazza
    Year: 2012
    Stability Analysis of Biological Network Topologies during Stochastic Simulation
    SIMUTOOLS
    ICST
    DOI: 10.4108/icst.simutools.2011.245590
Davide Prandi1,*, Tommaso Mazza2
  • 1: CoSBi
  • 2: Centre for Integrative Biology (CIBIO) University of Trento
*Contact email: prandi@cosbi.eu

Abstract

Recent advances in the stochastic simulation of biological systems have exploited the weighted dependency di-graph as a compact representation of the computational workload. It was largely used to represent the causal relationships among reactions and then to determine their cause-e ect implica- tions. Although critical for several applications, the topol- ogy of the dependency graph has been little studied so far. Here, we make use of some network topology indices to de- tect and characterize the important reactions of two real case studies. We measure the stability of such indices over time and make a case for considering them in parallel stochastic simulation.